Endophytic Burkholderia sp. SSG as a potential biofertilizer promoting boxwood growth
Background Burkholderia sp. SSG is a bacterial endophyte isolated from boxwood leaves showing a resistant response to infection by the boxwood blight pathogen Calonectria pseudonaviculata. SSG acted as a protective and curative biocontrol agent for boxwood blight and as a bio-sanitizer of disease inoculum in the field. Many gene clusters involved in antibiotic production and plant growth promotion (PGP) were found in the genome, giving this endophyte great application potential as a treatment for plant protection. However, the PGP features have not been documented. This study investigated the plant growth promotion activity of SSG in boxwood. Methods To determine whether SSG is a plant growth promoting bacterium, four PGP traits, auxin and siderophore production, nitrogen fixation and phosphate solubilization, were examined in the laboratory with colorimetric or agar plate assays. The plant growth promoting activity of SSG was tested on three boxwood varieties characterized by slow, intermediate and fast growth rates, namely Justin Brouwers, Buddy and Winter Gem, respectively. These plants were drenched with an SSG cell suspension or water and washed plant weight was compared before and after treatment to determine growth changes after 10 months. Results The SSG culture was sustainable on nitrogen free media, suggesting that SSG may fix atmospheric nitrogen. It was also a strong phosphate solubilizer and a potent siderophore and indole-3-acetic acid (IAA) producer. Significant growth promotion was observed on boxwood cultivars Justin Brouwers, Buddy and Winter Gem 10 months after plant roots were drenched with SSG cells. The growth rate of treated plants was 76.1, 58.3, and 37.3% higher than that of the control, respectively. The degree of growth promotion was significantly different among plant varieties, notably more pronounced with the slow and intermediate growers. This study demonstrates that the SSG bacterium has multiple PGP traits and is a prospective plant biofertilizer.
Kong et al. (2020) Endophytic Burkholderia sp. SSG as a potential biofertilizer promoting boxwood growth. PeerJ 8:e9547 https://doi.org/10.7717/peerj.9547
Whole mitochondrial genome sequence and phylogenetic relationships of Williams’s jerboa (Scarturus williamsi) from Turkey
Williams’s jerboa (Scarturus williamsi), a medium-sized jerboa distributed in Anatolia and its adjacent regions, is a member of the four- and five-toed jerboas found mostly in Asia. Disagreements about the taxonomy of this taxon at the genus/species level continue to exist. Here, we report the first effort to sequence and assemble the mitochondrial genome of Williams’s jerboa from Turkey. The mitochondrial genome of S. williamsi was 16,653 bp in total length and contained 13 protein-coding genes (PCGs), 22 transfer RNAs (tRNAs), two ribosomal RNAs (rRNAs), and two non-coding regions (the D-loop and OL region) with intergenic spacer. All of the genes, except ND6 and eight tRNAs, were encoded on the heavy chain strand, similar to the features of mitogenomes of other rodents. When compared with all available rodent mitochondrial genomes, Williams’s jerboa showed (1) a serine deletion at the 3′-end of the ATP8 gene, (2) the ND5 gene terminated with a TAG codon and (3) a tandem repeat cluster (273 bp in length) in the control region. Williams’s jerboa and Siberian jerboa grouped as sister taxa despite the high genetic distance (17.6%) between them, belonging to Allactaginae. This result is consistent with the latest pre-revision, which suggests that Williams’s jerboa and the Siberian jerboa may belong to separate genera, as Scarturus and Orientallactaga, respectively. The present study provides a reference mitochondrial genome for Williams’s jerboa for further molecular studies of other species of Dipodoidea and Rodentia.
İbiş (2020) Whole mitochondrial genome sequence and phylogenetic relationships of Williams’s jerboa (Scarturus williamsi) from Turkey. PeerJ 8:e9569 https://doi.org/10.7717/peerj.9569
Chlorine-based DUWL disinfectant leads to a different microbial composition of water derived biofilms compared to H2O2-based chemical disinfectants in vitro
Background Biofilm formation in dental unit waterlines (DUWL) may lead to health risks for dental staff and patients. Therefore, dental unit waterlines need to be disinfected, for instance by using chemical disinfectants. However, the application of chemical disinfectants may lead to the selection of specific microorganisms. Therefore, the aim of our study was to assess the microbial composition of water-derived biofilms, after a continuous exposure to maintenance doses of commercially available chemical disinfectants, in vitro. Methods The AAA-model was used to grow water derived biofilms. The biofilms were subjected to the maintenance dose of each disinfectant. To determine the microbial composition, the V4 hypervariable region of the 16S rRNA gene was sequenced. The sequences were clustered in operational taxonomic units (OTUs). Results The bacterial composition of biofilms in all treatment groups differed significantly (PERMANOVA F = 4.441, p = 0.001). Pairwise comparisons revealed Anoxyl treated biofilms were significantly different from all groups (p = 0.0001). In the Anoxyl-treated biofilms, the relative abundance of Comamonadaceae and Sphingopyxis was high compared to the Dentosept, Green and Clean and Oxygenal groups. Conclusion We concluded that exposure to low doses of the chlorine-based chemical disinfectant Anoxyl led to a substantially different composition of water derived biofilms compared to biofilms exposed to H2O2-based chemical disinfectants.
Zemouri et al. (2020) Chlorine-based DUWL disinfectant leads to a different microbial composition of water derived biofilms compared to H2O2-based chemical disinfectants in vitro. PeerJ 8:e9503 https://doi.org/10.7717/peerj.9503
Decomposition of dinosaurian remains inferred by invertebrate traces on vertebrate bone reveal new insights into Late Jurassic ecology, decay, and climate in western Colorado
A survey of 2,368 vertebrate fossils from the Upper Jurassic Mygatt-Moore Quarry (MMQ) (Morrison Formation, Brushy Basin Member) in western Colorado revealed 2,161 bone surface modifications on 884 specimens. This is the largest, site-wide bone surface modification survey of any Jurassic locality. Traces made by invertebrate actors were common in the assemblage, second in observed frequency after vertebrate bite marks. Invertebrate traces are found on 16.174% of the total surveyed material and comprise 20.148% of all identified traces. Six distinct invertebrate trace types were identified, including pits and furrows, rosettes, two types of bioglyph scrapes, bore holes and chambers. A minimum of four trace makers are indicated by the types, sizes and morphologies of the traces. Potential trace makers are inferred to be dermestid or clerid beetles, gastropods, an unknown necrophagous insect, and an unknown osteophagus insect. Of these, only gastropods are preserved at the site as body fossils. The remaining potential trace makers are part of the hidden paleodiversity from the North American Late Jurassic Period, revealed only through this ichnologic and taphonomic analysis. Site taphonomy suggests variable, but generally slow burial rates that range from months up to 6 years, while invertebrate traces on exposed elements indicate a minimum residence time of five months for carcasses with even few preserved invertebrate traces. These traces provide insight into the paleoecology, paleoclimate, and site formation of the MMQ, especially with regards to residence times of the skeletal remains on the paleolandscape. Comprehensive taphonomic studies, like this survey, are useful in exploring patterns of paleoecology and site formation, but they are also rare in Mesozoic assemblages. Additional work is required to determine if 16.174% is typical of bulk-collected fossils from Jurassic ecosystems in North America, or if the MMQ represents an unusual locality.
McHugh et al. (2020) Decomposition of dinosaurian remains inferred by invertebrate traces on vertebrate bone reveal new insights into Late Jurassic ecology, decay, and climate in western Colorado. PeerJ 8:e9510 https://doi.org/10.7717/peerj.9510
Canine SOD1 harboring E40K or T18S mutations promotes protein aggregation without reducing the global structural stability
Amyotrophic lateral sclerosis (ALS) is a progressive and fatal neurodegenerative disease associated with aggregation of superoxide dismutase 1 (SOD1) protein. More than 160 mutations in human SOD1 have been identified in familial ALS and extensively characterized in previous studies. Here, we investigated the effects of T18S and E40K mutations on protein aggregation of canine SOD1. These two mutations are exclusively found in canine degenerative myelopathy (an ALS-like neurodegenerative disease in dogs), whose phenotype is unknown at the level of protein folding. Interestingly, the T18S and E40K mutations did not alter far-UV CD spectrum, enzymatic activity, or global structural stability of canine SOD1. However, thioflavin-T assay and transmission electron microscopy analysis revealed that these mutations promote formation of fibrous aggregates, in particular in the Cu2+/Zn2+-unbound state. These evidence suggested that the T18S and E40K mutations promote protein aggregation through a unique mechanism, possibly involving destabilization of the local structure, reduction of net negative charge, or production of disulfide-linked oligomers.
Kimura et al. (2020) Canine SOD1 harboring E40K or T18S mutations promotes protein aggregation without reducing the global structural stability. PeerJ 8:e9512 https://doi.org/10.7717/peerj.9512
Craniofacial characteristics of Syrian adolescents with Class II division 1 malocclusion: a retrospective study
Background Malocclusion characteristics vary across different ethnic groups and populations. Limited data are available regarding the characteristics of Syrian adolescents with Class II division 1 (Class II-1) malocclusion, and the recent inflow of Syrian refugees and immigrants into Europe and many areas worldwide demonstrate the need for updated studies to discover the craniofacial characteristics of these new immigrants. Objectives The present compound cephalometric and tooth-size study sought to assess the dentofacial morphology, upper-airway dimensions, and tooth-size characteristics of Syrian adolescents with Class II-1 malocclusion and compare the results with established Syrian population norms. Materials and Methods The study sample consisted of 43 Syrian patients including 24 females and 19 males with Class II-1 malocclusion (age: 14.3 (±1.5) years, mean (±SD)). Cephalometric radiographs and orthodontic casts were analyzed using special orthodontic software (OnyxCeph3™) and a universal digital caliper, respectively. Statistics were calculated using the SPSS software. Results In Syrian adolescents with Class II-1 malocclusion, the position of the mandible relative to the nasion perpendicular (mean (95% confidence interval)) was −11.01 (−12.45, −9.57) mm. Facial axis angle showed a negative value: −6.25 (−7.65, −4.85) degrees. An obtuse nasolabial angle was observed: 104.05 (101.77, 106.33) degrees. The average width of the upper pharynx was 11.50 (10.53, 12.47) mm; however, there was no prevalence of an upper-pharyngeal width of 5 mm or less. The average value of the anterior tooth-size ratio was 80.69 (79.85, 81.53) percent. In total, 39.5% of the investigated subjects had anterior ratios outside two standard deviations from Bolton’s norm, while 25.6% of the investigated subjects had anterior ratios outside two standard deviations from Syrian population norm. Conclusions In this study, the inter-maxillary discrepancy of Class II-1 Syrian adolescents was a consequence of their hyperdivergent facial pattern. The observed small pharyngeal widths were not clinically significant, while the anterior tooth-size discrepancy might be clinically relevant.
Al Ayoubi et al. (2020) Craniofacial characteristics of Syrian adolescents with Class II division 1 malocclusion: a retrospective study. PeerJ 8:e9545 https://doi.org/10.7717/peerj.9545
Biofilm released cells can easily be obtained in a fed-batch system using ica+ but not with ica- isolates
Staphylococcus epidermidis is one of the major opportunistic bacterial pathogens in healthcare facilities, mainly due to its strong ability to form biofilms in the surface of indwelling medical devices. To study biofilms under in vitro conditions, both fed-batch and flow systems are widely used, with the first being the most frequent due to their low cost and ease of use. Aim To assess if a fed-batch system previously developed to obtain biofilm released cells (Brc) from strong biofilm producing S. epidermidis isolates could also be used to obtain and characterize Brc from isolates with lower abilities to form biofilms. Methodology The applicability of a fed-batch system to obtain Brc from biofilms of 3 ica+ and 3 ica− isolates was assessed by quantifying the biofilm and Brc biomass by optical density (OD) and colony-forming units (CFU) measurements. The effect of media replacement procedures of fed-batch systems on the amount of biofilm was determined by quantifying the biofilm and biofilm bulk fluid, by CFU, after consecutive washing steps. Results The fed-batch model was appropriate to obtain Brc from ica+ isolates, that presented a greater ability to form biofilms and release cells. However, the same was not true for ica− isolates, mainly because the washing procedure would physically remove a significant number of cells from the biofilm. Conclusions This study demonstrates that a fed-batch system is only feasible to be used to obtain Brc from S. epidermidis when studying strong and cohesive biofilm-forming isolates.
Gaio et al. (2020) Biofilm released cells can easily be obtained in a fed-batch system using ica+ but not with ica- isolates. PeerJ 8:e9549 https://doi.org/10.7717/peerj.9549
Changes of diazotrophic communities in response to cropping systems in a Mollisol of Northeast China
Nitrogen-fixing microorganisms play important roles in N cycling. However, knowledge related to the changes in the diazotrophic community in response to cropping systems is still rudimentary. In this study, the nifH gene was used to reveal the abundance and community compositions of diazotrophs in the cropping systems of continuous cropping of corn (CC) and soybean (SS) and soybean-corn rotation for growing corn (CSC) and soybean (SCS) in a black soil of Northeast China. The results showed that the abundance of the nifH gene was significantly higher in cropping soybean than in cropping corn under the same cropping system, while remarkably increased in the rotation system under the same crop. The Shannon index in the CC treatment was significantly higher than that in the other treatments, but the OTU number and Chao1 index had no significant change among the four treatments. Bradyrhizobium japonicum was the dominant diazotrophic species, and its relative abundance was at the lowest value in the CC treatment. In contrast, Skermanella sp. had the highest relative abundance in the CC treatment. A PCoA showed that the diazotrophic communities were separated between different cropping systems, and the variation caused by continuous corn cropping was the largest. Among the tested soil properties, the soil available phosphorus was a primary factor in determining diazotrophic community compositions. Overall, the findings of this study highlighted that the diazotrophic communities in black soils are very sensitive to cropping systems.
Zou et al. (2020) Changes of diazotrophic communities in response to cropping systems in a Mollisol of Northeast China. PeerJ 8:e9550 https://doi.org/10.7717/peerj.9550
Beyond loot boxes: a variety of gambling-like practices in video games are linked to both problem gambling and disordered gaming
A variety of practices have recently emerged which relate to both video games and gambling. These range from opening loot boxes, to esports betting, real-money video gaming, token wagering, and social casino spending. It is unknown either how harmful or how widespread many of these activities are. A sample of 1,081 adults from the UK aged 18+ was therefore recruited. This sample was purposively recruited via quota sampling to represent the UK population in terms of sex, age, and ethnicity. Engagement in all forms of gaming-related practices were significantly associated with both problem gambling and disordered gaming. A total of 18.5% of the sample had engaged in these activities at least once in the new year. These results suggest a convergent ecosystem of practices that relate to both video games and gambling. Engagement in each of these activities is linked to problem gambling. However, it remains unclear whether engagement in these activities causes problem gambling.
Zendle (2020) Beyond loot boxes: a variety of gambling-like practices in video games are linked to both problem gambling and disordered gaming. PeerJ 8:e9466 https://doi.org/10.7717/peerj.9466
Identification of potential biomarkers and their clinical significance in gastric cancer using bioinformatics analysis methods
Background Alternative splicing (AS) is an important mechanism for regulating gene expression and proteome diversity. Tumor-alternative splicing can reveal a large class of new splicing-associated potential new antigens that may affect the immune response and can be used for immunotherapy. Methods The RNA-seq transcriptome data and clinical information of stomach adenocarcinoma (STAD) cohort were downloaded from The Cancer Genome Atlas (TCGA) database data portal, and data of splicing events were obtained from the SpliceSeq database. Predicting genes were validated by Asian cancer research group (ACRG) cohort and Oncomine database. RT-qPCR was used to analysis the expression of ECT2 in STAD. Results A total of 32,166 AS events were identified, among which 2,042 AS events were significantly associated with patients survival. Biological pathway analysis indicated that these genes play an important role in regulating gastric cancer-related processes such as GTPase activity and PI3K-Akt signaling pathway. Next, we derived a risk signature, using alternate acceptor, that is an independent prognostic marker. Moreover, high ECT2 expression was associated with poorer prognosis in STAD. Multivariate survival analysis demonstrated that high ECT2 expression was an independent risk factor for overall survival. Gene set enrichment analysis revealed that high ECT2 expression was enriched for hallmarks of malignant tumors. The ACRG cohort and Oncomine also showed that high ECT2 expression was associated with poorer prognosis in gastric cancer patients. Finally, RT-qPCR showed ECT2 expression was higher in STAD compared to the normal tissues. Conclusion This study excavated the alternative splicing events in gastric cancer, and found ECT2 might be a biomarkers for diagnosis and prognosis.
Liu et al. (2020) Identification of potential biomarkers and their clinical significance in gastric cancer using bioinformatics analysis methods. PeerJ 8:e9174 https://doi.org/10.7717/peerj.9174